A few more unrelated suggestions:
1. Focus Fire
I think it would be cool if the player could focus all of there fire on a single portion of a ship, and then be given a reward for doing so. If a ship was disabled with minimal armor damage, it would lead to extra loot at the end of a battle, and possibly a ship that wouldn't need 100% repaired if you can successfully board it.
2. Missile Range Hullmod
We have hullmods that increase the range of ballistic and energy weapons, why not missiles?
3. Ship "Hull" Bonuses
More than a few times, I'm towing around a ship I just boarded simply to repair it and sell it at the next station I happen by. It would be nice if ships that have no OP spent get a few small bonuses (increased speed/maneuverability, increased repair rate, decreased skeleton crew requirements). They are still useless in combat, but you take a little less penalty for dragging it to a station.
EDIT:
Oh, and one more:
4. All Weapons Autofire
If I set all of my weapon groups to autofire, and I make sure that Weapon Group 1 has no weapons associated with it, please don't make the weapon auto grouping shove something back in to the first weapon group. I would like all of my weapons to be able to autofire from the start of the battle so that I don't end up in a firefight and wonder why all of my main weapons aren't firing like they are supposed to.